diff --git a/.classpath b/.classpath
index 1e8fddb84..115baaf13 100644
--- a/.classpath
+++ b/.classpath
@@ -1,8 +1,6 @@
-
-
@@ -52,7 +50,6 @@
-
@@ -109,5 +106,6 @@
+
diff --git a/.codecov.yml b/.codecov.yml
index 42c0d62b4..b75b4f7a4 100644
--- a/.codecov.yml
+++ b/.codecov.yml
@@ -26,5 +26,4 @@ comment:
require_changes: no
ignore:
- - "build"
- "deployment"
diff --git a/.gitattributes b/.gitattributes
new file mode 100644
index 000000000..00a51aff5
--- /dev/null
+++ b/.gitattributes
@@ -0,0 +1,6 @@
+#
+# https://help.github.com/articles/dealing-with-line-endings/
+#
+# These are explicitly windows files and should use crlf
+*.bat text eol=crlf
+
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index aab241b1a..fa95c318a 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -49,13 +49,13 @@ jobs:
mongo: 'mongodb-linux-x86_64-ubuntu2204-7.0.4'
minio: '2019-05-23T00-29-34Z'
wired_tiger: 'true'
- ant_test: 'test_quick_coverage'
+ gradle_test: 'testQuick'
# the current production setup
- java: '11'
mongo: 'mongodb-linux-x86_64-3.6.13'
minio: '2019-05-23T00-29-34Z'
wired_tiger: 'false'
- ant_test: 'test_quick_coverage'
+ gradle_test: 'testQuick'
steps:
- uses: actions/checkout@v3
@@ -84,10 +84,6 @@ jobs:
# move to parent dir of homedir to install binaries etc
cd ..
- # set up jars
- git clone https://github.com/kbase/jars
- export JARSDIR=$(pwd)/jars/lib/jars/
-
# set up arango
export ARANGODB_VER=3.9.1
export ARANGODB_V=39
@@ -153,8 +149,7 @@ jobs:
- name: Run tests
shell: bash
run: |
- ant javadoc
- ant ${{matrix.ant_test}}
+ ./gradlew ${{matrix.gradle_test}}
- name: Upload coverage to Codecov
uses: codecov/codecov-action@v3
diff --git a/build.gradle b/build.gradle
new file mode 100644
index 000000000..9b787744c
--- /dev/null
+++ b/build.gradle
@@ -0,0 +1,245 @@
+/*
+ * This file was generated by the Gradle 'init' task.
+ */
+
+plugins {
+ id 'java'
+ id 'war'
+ id 'jacoco'
+ id 'org.ajoberstar.grgit' version '4.1.1'
+ id 'com.github.johnrengelman.shadow' version '8.1.1'
+}
+
+// TODO NOW test shadow jar works in groups - remove JNA - commit 2
+// TODO NOW get docserver working in WAR and test in docker-compose <- edit to start test server - commit 3
+// TODO NOW client jar - commit 4
+// TODO NOW client jar javadoc - needs java_common source - commit 4
+// TODO NOW schema updater script - commit 5
+// TODO NOW sdk-compile all, java, and docs - commit 6
+// TODO NOW handle the git commit the same way as auth does - commit 7
+// TODO NOW delete build.xml, , and Makefile - commit 8
+// TODO NOW run tests from Eclipse w/o specifying classpath manually & remove sourceSets & claspath - commit 9
+
+repositories {
+ mavenCentral()
+}
+compileJava {
+ options.release = 11
+}
+
+// jacoco doesn't play nicely with test tasks not named "test"
+def coverageFile = layout -> layout.buildDirectory.file('jacoco/coverage.exec').get()
+
+tasks.withType(Test) {
+ /*
+ * TODO TEST Figure out why tests fail without this and remove. Might have something to do
+ * with the stfuLoggers() call in many of the tests, might kill logging for tests that
+ * require it
+ * Although it seems to make Mongo start up correctly as well which is odd
+ */
+ forkEvery = 1
+ /*
+ * TODO TEST split tests into mongo wrapper tests & all other tests (incl. integration).
+ * Set up GHA to run the non-mongo tests with a single version of mongo and run the
+ * mongo tests with matrixed mongo versions. Combine coverage at the end somehow
+ */
+ systemProperty "test.cfg", "./test.cfg"
+ maxHeapSize = "3G"
+ testLogging {
+ exceptionFormat = 'full'
+ showStandardStreams = true
+ }
+ filter {
+ // gradle thinks that classes annotated with @RunWith are tests
+ excludeTestsMatching "*Tester"
+ }
+ jacoco {
+ destinationFile = coverageFile(layout).asFile
+ }
+ finalizedBy jacocoTestReport
+}
+
+jacocoTestReport {
+ getExecutionData().setFrom(files(coverageFile(layout)))
+ reports {
+ xml.required = true
+ csv.required = true
+ }
+}
+
+test {
+ // no special config needed
+}
+
+task testQuick(type: Test) {
+ // for Gradle 9.0 compatibility
+ testClassesDirs = testing.suites.test.sources.output.classesDirs
+ classpath = testing.suites.test.sources.runtimeClasspath
+
+ filter {
+ excludeTestsMatching "*LongTest"
+ }
+}
+
+// Custom java project layout
+sourceSets {
+ main {
+ java {
+ srcDirs = ["src"]
+ exclude '**/test/**'
+ }
+ }
+ test {
+ java {
+ srcDirs = ["src"]
+ include '**/test/**'
+ }
+ resources {
+ srcDirs = ["src"]
+ include "**/*.properties"
+ include '**/*.spec'
+ include '**/*instance.*'
+ include '**/*.instance*'
+ include '**/*.html'
+ include '**/*.css'
+ include '**/*.gif'
+ include '**/*.js'
+ include '**/*.png'
+ include '**/*.txt'
+ include '**/*.weirdsuffix'
+ }
+ }
+}
+
+javadoc {
+ options {
+ links "https://docs.oracle.com/en/java/javase/11/docs/api/"
+ links "https://www.javadoc.io/doc/com.fasterxml.jackson.core/jackson-core/2.9.9/"
+ links "https://www.javadoc.io/doc/com.fasterxml.jackson.core/jackson-databind/2.9.9/"
+ }
+}
+
+war {
+ webXml = file('war/web.xml')
+}
+
+configurations {
+ // can't directly access testImplementation, so extend and access
+ testimpl.extendsFrom testImplementation
+}
+
+def fromURL = { url, name ->
+ File file = new File("$buildDir/download/${name}.jar")
+ file.parentFile.mkdirs()
+ if (!file.exists()) {
+ new URL(url).withInputStream { downloadStream ->
+ file.withOutputStream { fileOut ->
+ fileOut << downloadStream
+ }
+ }
+ }
+ files(file.absolutePath)
+}
+
+dependencies {
+
+ // ### General application dependencies ###
+
+ implementation fromURL(
+ 'https://github.com/kbase/jars/raw/master/lib/jars/kbase/auth/kbase-auth-0.4.4.jar',
+ 'kbase-auth-0.4.4'
+ )
+ implementation fromURL(
+ 'https://github.com/kbase/jars/raw/master/lib/jars/kbase/kidl/kbase-kidl-parser-1409261812-7863aef.jar',
+ 'kbase-kidl-parser-1409261812-7863aef'
+ )
+ implementation 'com.fasterxml.jackson.core:jackson-annotations:2.9.9'
+ implementation 'com.fasterxml.jackson.core:jackson-core:2.9.9'
+ implementation 'com.fasterxml.jackson.core:jackson-databind:2.9.9'
+ implementation 'org.ini4j:ini4j:0.5.2'
+ implementation 'commons-io:commons-io:2.4'
+ implementation 'org.apache.commons:commons-lang3:3.1'
+ implementation 'commons-codec:commons-codec:1.8'
+ implementation 'info.picocli:picocli:4.6.1'
+ implementation 'org.mongodb:mongodb-driver-core:4.11.1'
+ implementation 'org.mongodb:mongodb-driver-sync:4.11.1'
+ implementation 'org.mongodb:bson-record-codec:4.11.1'
+ implementation 'org.mongodb:bson:4.11.1'
+ implementation 'org.slf4j:slf4j-api:1.7.30'
+ implementation 'ch.qos.logback:logback-classic:1.1.2'
+ implementation 'com.google.guava:guava:14.0.1'
+ implementation 'com.github.ben-manes.caffeine:caffeine:2.9.3'
+ implementation 'org.apache.kafka:kafka-clients:2.1.0'
+ implementation fromURL(
+ 'https://github.com/kbase/jars/raw/master/lib/jars/kbase/handle/AbstractHandleClient-1.0.0.jar',
+ 'AbstractHandleClient-1.0.0'
+ )
+ implementation fromURL(
+ 'https://github.com/kbase/jars/raw/master/lib/jars/kbase/sample/SampleServiceClient-0.1.1.jar',
+ 'SampleServiceClient-0.1.1'
+ )
+
+ // ### Server dependencies, specifically for java_common JsonServerServlet ###
+
+ implementation fromURL(
+ 'https://github.com/kbase/jars/raw/master/lib/jars/kbase/common/kbase-common-0.2.0.jar',
+ 'kbase-common-0.2.0'
+ )
+ // joda-time is required for kbase-common and syslog4j
+ implementation 'joda-time:joda-time:2.2'
+ // this is OOOOOOLD. But that probably means updating java_common
+ implementation 'org.eclipse.jetty.aggregate:jetty-all:7.0.0.v20091005'
+ implementation 'javax.servlet:servlet-api:2.5'
+ implementation 'javax.annotation:javax.annotation-api:1.3.2'
+ // Syslog4j 0.9.46 doesn't appear to be available on Maven. It apparently lives in
+ // a JetBrains artifact server, but that's too much trouble and there's only one version there
+ // anyway.
+ // https://mvnrepository.com/artifact/org.jetbrains/syslog4j/0.9.46
+ // Need to rework the java common logger to not use syslog4j at all since it's abandonware
+ // and has a ton of CVEs, even in the newer versions.
+ implementation fromURL(
+ 'https://github.com/kbase/jars/raw/master/lib/jars/syslog4j/syslog4j-0.9.46.jar',
+ 'syslog4j-0.9.46'
+ )
+ // needed for syslog4j
+ implementation 'net.java.dev.jna:jna:3.4.0'
+
+ // ### Blobstore / Shock client and dependencies ###
+
+ implementation fromURL(
+ 'https://github.com/kbase/jars/raw/master/lib/jars/kbase/shock/shock-client-0.1.0.jar',
+ 'shock-client-0.1.0'
+ )
+ implementation 'org.apache.httpcomponents:httpclient:4.5.9'
+ implementation 'org.apache.httpcomponents:httpmime:4.5.8'
+
+ // ### Amazon S3 ###
+
+ implementation('software.amazon.awssdk:s3:2.17.214') {
+ exclude module: 'apache-client'
+ exclude module: 'netty-nio-client'
+ }
+ implementation 'software.amazon.awssdk:url-connection-client:2.17.214'
+
+ // ### Test ###
+
+ testImplementation 'junit:junit:4.12'
+ testImplementation 'org.hamcrest:hamcrest-core:1.3'
+ testImplementation 'com.github.zafarkhaja:java-semver:0.9.0'
+ testImplementation 'nl.jqno.equalsverifier:equalsverifier:3.1.10'
+ testImplementation 'com.arangodb:arangodb-java-driver:6.7.2'
+ testImplementation 'org.mockito:mockito-core:3.0.0'
+
+ testImplementation 'commons-lang:commons-lang:2.4'
+ testImplementation fromURL(
+ 'https://github.com/kbase/jars/raw/master/lib/jars/kbase/auth2/kbase-auth2-test-shadow-all-0.7.0.jar',
+ 'kbase-auth2-test-shadow-all-0.7.0'
+ )
+}
+
+task showTestClassPath {
+ doLast {
+ configurations.testimpl.each { println it }
+ }
+}
+
diff --git a/docsource/releasenotes.rst b/docsource/releasenotes.rst
index 6d67c630c..9e1afb90f 100644
--- a/docsource/releasenotes.rst
+++ b/docsource/releasenotes.rst
@@ -8,7 +8,10 @@ VERSION: 0.14.3 (Released 2/22/2024)
UPDATES:
-* The MongoDB clients have been updated to the most recent version and the service tested against Mongo 7.
+* The MongoDB clients have been updated to the most recent version and the service tested
+ against Mongo 7.
+* Gradle has replaced Ant as the build tool. As a consequence, all the built artifacts are now
+ located in the build directory, including the ``update_workspace_database_schema`` script.
VERSION: 0.14.2 (Released 11/9/2023)
diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar
new file mode 100644
index 000000000..41d9927a4
Binary files /dev/null and b/gradle/wrapper/gradle-wrapper.jar differ
diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
new file mode 100644
index 000000000..17655d0ef
--- /dev/null
+++ b/gradle/wrapper/gradle-wrapper.properties
@@ -0,0 +1,5 @@
+distributionBase=GRADLE_USER_HOME
+distributionPath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.6-bin.zip
+zipStoreBase=GRADLE_USER_HOME
+zipStorePath=wrapper/dists
diff --git a/gradlew b/gradlew
new file mode 100755
index 000000000..1b6c78733
--- /dev/null
+++ b/gradlew
@@ -0,0 +1,234 @@
+#!/bin/sh
+
+#
+# Copyright © 2015-2021 the original authors.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# https://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+##############################################################################
+#
+# Gradle start up script for POSIX generated by Gradle.
+#
+# Important for running:
+#
+# (1) You need a POSIX-compliant shell to run this script. If your /bin/sh is
+# noncompliant, but you have some other compliant shell such as ksh or
+# bash, then to run this script, type that shell name before the whole
+# command line, like:
+#
+# ksh Gradle
+#
+# Busybox and similar reduced shells will NOT work, because this script
+# requires all of these POSIX shell features:
+# * functions;
+# * expansions «$var», «${var}», «${var:-default}», «${var+SET}»,
+# «${var#prefix}», «${var%suffix}», and «$( cmd )»;
+# * compound commands having a testable exit status, especially «case»;
+# * various built-in commands including «command», «set», and «ulimit».
+#
+# Important for patching:
+#
+# (2) This script targets any POSIX shell, so it avoids extensions provided
+# by Bash, Ksh, etc; in particular arrays are avoided.
+#
+# The "traditional" practice of packing multiple parameters into a
+# space-separated string is a well documented source of bugs and security
+# problems, so this is (mostly) avoided, by progressively accumulating
+# options in "$@", and eventually passing that to Java.
+#
+# Where the inherited environment variables (DEFAULT_JVM_OPTS, JAVA_OPTS,
+# and GRADLE_OPTS) rely on word-splitting, this is performed explicitly;
+# see the in-line comments for details.
+#
+# There are tweaks for specific operating systems such as AIX, CygWin,
+# Darwin, MinGW, and NonStop.
+#
+# (3) This script is generated from the Groovy template
+# https://github.com/gradle/gradle/blob/master/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
+# within the Gradle project.
+#
+# You can find Gradle at https://github.com/gradle/gradle/.
+#
+##############################################################################
+
+# Attempt to set APP_HOME
+
+# Resolve links: $0 may be a link
+app_path=$0
+
+# Need this for daisy-chained symlinks.
+while
+ APP_HOME=${app_path%"${app_path##*/}"} # leaves a trailing /; empty if no leading path
+ [ -h "$app_path" ]
+do
+ ls=$( ls -ld "$app_path" )
+ link=${ls#*' -> '}
+ case $link in #(
+ /*) app_path=$link ;; #(
+ *) app_path=$APP_HOME$link ;;
+ esac
+done
+
+APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit
+
+APP_NAME="Gradle"
+APP_BASE_NAME=${0##*/}
+
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
+
+# Use the maximum available, or set MAX_FD != -1 to use that value.
+MAX_FD=maximum
+
+warn () {
+ echo "$*"
+} >&2
+
+die () {
+ echo
+ echo "$*"
+ echo
+ exit 1
+} >&2
+
+# OS specific support (must be 'true' or 'false').
+cygwin=false
+msys=false
+darwin=false
+nonstop=false
+case "$( uname )" in #(
+ CYGWIN* ) cygwin=true ;; #(
+ Darwin* ) darwin=true ;; #(
+ MSYS* | MINGW* ) msys=true ;; #(
+ NONSTOP* ) nonstop=true ;;
+esac
+
+CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
+
+
+# Determine the Java command to use to start the JVM.
+if [ -n "$JAVA_HOME" ] ; then
+ if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
+ # IBM's JDK on AIX uses strange locations for the executables
+ JAVACMD=$JAVA_HOME/jre/sh/java
+ else
+ JAVACMD=$JAVA_HOME/bin/java
+ fi
+ if [ ! -x "$JAVACMD" ] ; then
+ die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+ fi
+else
+ JAVACMD=java
+ which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+fi
+
+# Increase the maximum file descriptors if we can.
+if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
+ case $MAX_FD in #(
+ max*)
+ MAX_FD=$( ulimit -H -n ) ||
+ warn "Could not query maximum file descriptor limit"
+ esac
+ case $MAX_FD in #(
+ '' | soft) :;; #(
+ *)
+ ulimit -n "$MAX_FD" ||
+ warn "Could not set maximum file descriptor limit to $MAX_FD"
+ esac
+fi
+
+# Collect all arguments for the java command, stacking in reverse order:
+# * args from the command line
+# * the main class name
+# * -classpath
+# * -D...appname settings
+# * --module-path (only if needed)
+# * DEFAULT_JVM_OPTS, JAVA_OPTS, and GRADLE_OPTS environment variables.
+
+# For Cygwin or MSYS, switch paths to Windows format before running java
+if "$cygwin" || "$msys" ; then
+ APP_HOME=$( cygpath --path --mixed "$APP_HOME" )
+ CLASSPATH=$( cygpath --path --mixed "$CLASSPATH" )
+
+ JAVACMD=$( cygpath --unix "$JAVACMD" )
+
+ # Now convert the arguments - kludge to limit ourselves to /bin/sh
+ for arg do
+ if
+ case $arg in #(
+ -*) false ;; # don't mess with options #(
+ /?*) t=${arg#/} t=/${t%%/*} # looks like a POSIX filepath
+ [ -e "$t" ] ;; #(
+ *) false ;;
+ esac
+ then
+ arg=$( cygpath --path --ignore --mixed "$arg" )
+ fi
+ # Roll the args list around exactly as many times as the number of
+ # args, so each arg winds up back in the position where it started, but
+ # possibly modified.
+ #
+ # NB: a `for` loop captures its iteration list before it begins, so
+ # changing the positional parameters here affects neither the number of
+ # iterations, nor the values presented in `arg`.
+ shift # remove old arg
+ set -- "$@" "$arg" # push replacement arg
+ done
+fi
+
+# Collect all arguments for the java command;
+# * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $GRADLE_OPTS can contain fragments of
+# shell script including quotes and variable substitutions, so put them in
+# double quotes to make sure that they get re-expanded; and
+# * put everything else in single quotes, so that it's not re-expanded.
+
+set -- \
+ "-Dorg.gradle.appname=$APP_BASE_NAME" \
+ -classpath "$CLASSPATH" \
+ org.gradle.wrapper.GradleWrapperMain \
+ "$@"
+
+# Use "xargs" to parse quoted args.
+#
+# With -n1 it outputs one arg per line, with the quotes and backslashes removed.
+#
+# In Bash we could simply go:
+#
+# readarray ARGS < <( xargs -n1 <<<"$var" ) &&
+# set -- "${ARGS[@]}" "$@"
+#
+# but POSIX shell has neither arrays nor command substitution, so instead we
+# post-process each arg (as a line of input to sed) to backslash-escape any
+# character that might be a shell metacharacter, then use eval to reverse
+# that process (while maintaining the separation between arguments), and wrap
+# the whole thing up as a single "set" statement.
+#
+# This will of course break if any of these variables contains a newline or
+# an unmatched quote.
+#
+
+eval "set -- $(
+ printf '%s\n' "$DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS" |
+ xargs -n1 |
+ sed ' s~[^-[:alnum:]+,./:=@_]~\\&~g; ' |
+ tr '\n' ' '
+ )" '"$@"'
+
+exec "$JAVACMD" "$@"
diff --git a/server_scripts/README.md b/server_scripts/README.md
new file mode 100644
index 000000000..6c7181b3b
--- /dev/null
+++ b/server_scripts/README.md
@@ -0,0 +1,4 @@
+These scripts are deprecated in favor of a tomcat based deployment via Dockerfile.
+
+TODO: Redo the dockerfile with a clean install of an updated Tomcat installation
+TODO: Redo server startup instructions in the docs cleanly, step by step
\ No newline at end of file
diff --git a/settings.gradle b/settings.gradle
new file mode 100644
index 000000000..957ae4c25
--- /dev/null
+++ b/settings.gradle
@@ -0,0 +1,11 @@
+/*
+ * This file was generated by the Gradle 'init' task.
+ *
+ * The settings file is used to specify which projects to include in your build.
+ *
+ * Detailed information about configuring a multi-project build in Gradle can be found
+ * in the user manual at https://docs.gradle.org/7.4.2/userguide/multi_project_builds.html
+ * This project uses @Incubating APIs which are subject to change.
+ */
+
+rootProject.name = 'workspace_deluxe'
diff --git a/src/us/kbase/common/test/TestCommon.java b/src/us/kbase/common/test/TestCommon.java
index 85e7fc6d8..e89b4f052 100644
--- a/src/us/kbase/common/test/TestCommon.java
+++ b/src/us/kbase/common/test/TestCommon.java
@@ -50,8 +50,6 @@ public class TestCommon {
public static final String ARANGOEXE = "test.arango.exe";
public static final String ARANGOJS = "test.arango.js";
- public static final String JARS_PATH = "test.jars.dir";
-
public static final String TEST_TEMP_DIR = "test.temp.dir";
public static final String KEEP_TEMP_DIR = "test.temp.dir.keep";
@@ -167,10 +165,6 @@ public static Path getSampleServiceDir() {
return Paths.get(getTestProperty(SAMPLE_SERVICE_DIR));
}
- public static Path getJarsDir() {
- return Paths.get(getTestProperty(JARS_PATH));
- }
-
public static boolean getDeleteTempFiles() {
return !"true".equals(getTestProperty(KEEP_TEMP_DIR));
}
diff --git a/src/us/kbase/typedobj/core/NullJsonGenerator.java b/src/us/kbase/typedobj/core/NullJsonGenerator.java
index 37c45470a..ecc57981a 100644
--- a/src/us/kbase/typedobj/core/NullJsonGenerator.java
+++ b/src/us/kbase/typedobj/core/NullJsonGenerator.java
@@ -240,6 +240,7 @@ public int getFeatureMask() {
}
@Override
+ @Deprecated
public JsonGenerator setFeatureMask(int values) {
return null;
}
diff --git a/src/us/kbase/typedobj/db/KidlUtil.java b/src/us/kbase/typedobj/db/KidlUtil.java
index 02bfc00a6..d90b675c2 100644
--- a/src/us/kbase/typedobj/db/KidlUtil.java
+++ b/src/us/kbase/typedobj/db/KidlUtil.java
@@ -1,8 +1,5 @@
package us.kbase.typedobj.db;
-import static org.hamcrest.CoreMatchers.is;
-import static org.junit.Assert.assertThat;
-
import java.io.BufferedReader;
import java.io.IOException;
import java.io.StringReader;
@@ -37,30 +34,6 @@ public static boolean compareJson(Map parse1, Map parse2, String hea
return ok;
}
- public static boolean compareJsonSchemas(Map> schemas1,
- Map> schemas2, String header) throws IOException,
- JsonParseException, JsonMappingException, JsonGenerationException,
- Exception {
- boolean ok = true;
- assertThat(schemas1.keySet(), is(schemas2.keySet()));
- for (String moduleName : schemas1.keySet()) {
- assertThat(schemas1.get(moduleName).keySet(), is(schemas2.get(moduleName).keySet()));
- for (Map.Entry entry : schemas1.get(moduleName).entrySet()) {
- String schema1 = rewriteJson(entry.getValue());
- String schema2 = rewriteJson(schemas2.get(moduleName).get(entry.getKey()));
- if (!schema1.equals(schema2)) {
- ok = false;
- System.out.println(header + " (" + moduleName + "." + entry.getKey() + "):");
- System.out.println("--------------------------------------------------------");
- showDiff(schema1, schema2);
- System.out.println();
- System.out.println("*");
- }
- }
- }
- return ok;
- }
-
private static void showDiff(String origText, String newText) throws Exception {
List origLn = getLines(origText);
List newLn = getLines(newText);
diff --git a/src/us/kbase/typedobj/db/test/MongoTypeStorageTest.java b/src/us/kbase/typedobj/db/test/MongoTypeStorageTest.java
index e3a5afb04..930fd45cd 100644
--- a/src/us/kbase/typedobj/db/test/MongoTypeStorageTest.java
+++ b/src/us/kbase/typedobj/db/test/MongoTypeStorageTest.java
@@ -43,7 +43,6 @@ public static void setUp() throws Exception {
System.out.println("Started test mongo instance at localhost:" +
MONGO.getServerPort());
- @SuppressWarnings("resource")
final MongoClient mc = MongoClients.create("mongodb://localhost:" + MONGO.getServerPort());
MONGO_DB = mc.getDatabase("test_" + MongoTypeStorageTest.class.getSimpleName());
}
diff --git a/src/us/kbase/typedobj/db/test/TypeRegisteringTest.java b/src/us/kbase/typedobj/db/test/TypeRegisteringTest.java
index a71f7cd7a..2a89162fe 100644
--- a/src/us/kbase/typedobj/db/test/TypeRegisteringTest.java
+++ b/src/us/kbase/typedobj/db/test/TypeRegisteringTest.java
@@ -144,7 +144,6 @@ public static MongoDatabase createMongoDbConnection() throws Exception {
System.out.println("Using mongo temp dir " +
mongo.getTempDir());
}
- @SuppressWarnings("resource")
final MongoClient mcli = MongoClients.create("mongodb://localhost:" + mongo.getServerPort());
final MongoDatabase mdb = mcli.getDatabase("TypeRegisteringTest");
TestCommon.destroyDB(mdb);
diff --git a/src/us/kbase/workspace/database/Workspace.java b/src/us/kbase/workspace/database/Workspace.java
index a0b843f2b..f2513dccb 100644
--- a/src/us/kbase/workspace/database/Workspace.java
+++ b/src/us/kbase/workspace/database/Workspace.java
@@ -1244,7 +1244,7 @@ public List> getReferencingObjects(
return ret;
}
- /** @deprecated */
+ @Deprecated
public List getReferencingObjectCounts(
final WorkspaceUser user, final List loi)
throws WorkspaceCommunicationException, InaccessibleObjectException,
diff --git a/src/us/kbase/workspace/database/WorkspaceDatabase.java b/src/us/kbase/workspace/database/WorkspaceDatabase.java
index 53fc2a095..9f2873c03 100644
--- a/src/us/kbase/workspace/database/WorkspaceDatabase.java
+++ b/src/us/kbase/workspace/database/WorkspaceDatabase.java
@@ -442,7 +442,7 @@ Map getObjectIncomingReferences(
Set objs)
throws NoSuchObjectException, WorkspaceCommunicationException;
- /** @deprecated */
+ @Deprecated
Map getReferencingObjectCounts(
Set objects)
throws WorkspaceCommunicationException, NoSuchObjectException;
diff --git a/src/us/kbase/workspace/database/mongo/MongoWorkspaceDB.java b/src/us/kbase/workspace/database/mongo/MongoWorkspaceDB.java
index 9aba5ad06..8f5b6f9b2 100644
--- a/src/us/kbase/workspace/database/mongo/MongoWorkspaceDB.java
+++ b/src/us/kbase/workspace/database/mongo/MongoWorkspaceDB.java
@@ -2734,8 +2734,8 @@ public Map> getReferencingObjects(
private static final Set FLDS_REF_CNT = newHashSet(
Fields.OBJ_ID, Fields.OBJ_NAME, Fields.OBJ_DEL, Fields.OBJ_VCNT, Fields.OBJ_REFCOUNTS);
- /** @deprecated */
@Override
+ @Deprecated
public Map getReferencingObjectCounts(
final Set objects)
throws WorkspaceCommunicationException, NoSuchObjectException {
diff --git a/src/us/kbase/workspace/kbase/admin/AdministrationCommandSetInstaller.java b/src/us/kbase/workspace/kbase/admin/AdministrationCommandSetInstaller.java
index 7b263325e..07722c58c 100644
--- a/src/us/kbase/workspace/kbase/admin/AdministrationCommandSetInstaller.java
+++ b/src/us/kbase/workspace/kbase/admin/AdministrationCommandSetInstaller.java
@@ -11,7 +11,7 @@
import java.util.Optional;
import java.util.stream.Collectors;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
diff --git a/src/us/kbase/workspace/test/database/mongo/GridFSBlobStoreTest.java b/src/us/kbase/workspace/test/database/mongo/GridFSBlobStoreTest.java
index 4a0f308cd..e98e112f6 100644
--- a/src/us/kbase/workspace/test/database/mongo/GridFSBlobStoreTest.java
+++ b/src/us/kbase/workspace/test/database/mongo/GridFSBlobStoreTest.java
@@ -59,7 +59,6 @@ public static void setUpClass() throws Exception {
System.out.println("Using Mongo temp dir " +
mongo.getTempDir());
TestCommon.stfuLoggers();
- @SuppressWarnings("resource")
final MongoClient mongoClient = MongoClients.create("mongodb://localhost:" + mongo.getServerPort());
final MongoDatabase db = mongoClient.getDatabase("GridFSBackendTest");
gfs = GridFSBuckets.create(db);
diff --git a/src/us/kbase/workspace/test/database/mongo/MongoWorkspaceDBTest.java b/src/us/kbase/workspace/test/database/mongo/MongoWorkspaceDBTest.java
index c0242c697..602e7366f 100644
--- a/src/us/kbase/workspace/test/database/mongo/MongoWorkspaceDBTest.java
+++ b/src/us/kbase/workspace/test/database/mongo/MongoWorkspaceDBTest.java
@@ -117,7 +117,6 @@ public static void setup() throws Exception {
System.out.println("Started test mongo instance at localhost:" +
MONGO.getServerPort());
- @SuppressWarnings("resource")
final MongoClient mc = MongoClients.create("mongodb://localhost:" + MONGO.getServerPort());
MONGO_DB = mc.getDatabase("test_" + MongoWorkspaceDBTest.class.getSimpleName());
diff --git a/src/us/kbase/workspace/test/database/mongo/S3BlobStoreIntegrationTest.java b/src/us/kbase/workspace/test/database/mongo/S3BlobStoreIntegrationTest.java
index 8c3a3c1f4..250d80d56 100644
--- a/src/us/kbase/workspace/test/database/mongo/S3BlobStoreIntegrationTest.java
+++ b/src/us/kbase/workspace/test/database/mongo/S3BlobStoreIntegrationTest.java
@@ -68,7 +68,6 @@ public static void setUpClass() throws Exception {
System.out.println("Using Mongo temp dir " + mongoCon.getTempDir());
System.out.println("Started mongo server at localhost:" + mongoCon.getServerPort());
- @SuppressWarnings("resource")
MongoClient mongoClient = MongoClients.create("mongodb://localhost:" + mongoCon.getServerPort());
mongo = mongoClient.getDatabase("MinioBackendTest");
diff --git a/src/us/kbase/workspace/test/database/mongo/SchemaUpdaterTest.java b/src/us/kbase/workspace/test/database/mongo/SchemaUpdaterTest.java
index 5fec5968e..40298e6ea 100644
--- a/src/us/kbase/workspace/test/database/mongo/SchemaUpdaterTest.java
+++ b/src/us/kbase/workspace/test/database/mongo/SchemaUpdaterTest.java
@@ -12,7 +12,6 @@
import java.util.Arrays;
import java.util.Collections;
import java.util.Date;
-import java.util.HashSet;
import java.util.LinkedList;
import java.util.List;
import java.util.Set;
diff --git a/src/us/kbase/workspace/test/workspace/WorkspaceIntegrationWithGridFSTest.java b/src/us/kbase/workspace/test/workspace/WorkspaceIntegrationWithGridFSTest.java
index ffbb3681d..5a28058ca 100644
--- a/src/us/kbase/workspace/test/workspace/WorkspaceIntegrationWithGridFSTest.java
+++ b/src/us/kbase/workspace/test/workspace/WorkspaceIntegrationWithGridFSTest.java
@@ -114,7 +114,6 @@ public static void setUpClass() throws Exception {
System.out.println("Using Mongo temp dir " + MONGO.getTempDir());
System.out.println("Started test mongo instance at localhost: " + MONGO.getServerPort());
- @SuppressWarnings("resource")
final MongoClient mcli = MongoClients.create("mongodb://localhost:" + MONGO.getServerPort());
WSDB = mcli.getDatabase(WSDB_NAME);
TYPEDB = mcli.getDatabase(TYPEDB_NAME);
diff --git a/src/us/kbase/workspace/test/workspace/WorkspaceTester.java b/src/us/kbase/workspace/test/workspace/WorkspaceTester.java
index 1e4e6e3f3..d933fae52 100644
--- a/src/us/kbase/workspace/test/workspace/WorkspaceTester.java
+++ b/src/us/kbase/workspace/test/workspace/WorkspaceTester.java
@@ -204,7 +204,6 @@ public WorkspaceTester(
mongo.getServerPort());
}
if (!CONFIGS.containsKey(config)) {
- @SuppressWarnings("resource")
final MongoClient mcli = MongoClients.create("mongodb://localhost:" + mongo.getServerPort());
final MongoDatabase wsdb = mcli.getDatabase(DB_WS_NAME);
final MongoDatabase tdb = mcli.getDatabase(DB_TYPE_NAME);
diff --git a/test.cfg.example b/test.cfg.example
index a66c1312f..ea4f09a66 100644
--- a/test.cfg.example
+++ b/test.cfg.example
@@ -2,10 +2,6 @@
[Workspacetest]
-# The path to the jars dir inside the jars repo, e.g.
-# [path to jars repo]/lib/jars
-test.jars.dir =
-
# Minio exe file location
test.minio.exe = minio